title: ChIP-Seq N8 S159

city: singapore

first: Ser Yue

last: Loo

address: 60 biopolis street

country: Singapore

institute: Genome Institute of Singapore

summary: To understand the manner by which RAR and RXR program cell state transitions, we performed ChIP-seq to identify their compendium of target genes in an unbiased manner. We exposed the mesenchymal NAMEC8 and SUM159 cancer cells to retinoid treatment, followed by the genome-wide analyses of target gene binding sites for RXR, RAR, H3K27ac and p300. Exposure to bexarotene, a RXR ligand, led to a subset of genes that became bound by RXR, as well as RAR, since both could form heterodimers. These genes furthermore showed increases in p300 binding, and H3K27ac (histone 3, lysine 27 acetylation) modification, which marks gene enhancers.

overall_design: NAMEC8 and SUM159 were treated with DMSO or Bexarotene for 7days (ST) and 14 days (LT). They were then harvested and examined with 4 different antibodies.

first: Loo

last: Yue

first: Wilson

last: Tan


title: Sequencing of Danio rerio skin for 3 age groups

status: Public on Oct 19 2021

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

type: Expression profiling by high throughput sequencing

summary: Comparison of temporal gene expression profiles from Danio rerio skin. The RNA-seq data comprise 3 age groups at 5, 24 and 30 months.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 4 samples in 3 groups: 5 months (1 Samples), 24 months (2 Samples), 30 months (1 Samples)

first: Nils

last: Hartmann

first: Christoph

last: Englert

first: Steffen

last: Priebe

first: Otto

last: Witte

first: Christiane

last: Frahm

first: Madlen

last: Guenther

first: Rolf

last: Hühne

first: Marco

last: Groth

first: Matthias

last: Platzer


title: Zinc oxide Nanoparticles exposure impairs cranial neural crest development by inducing oxidant stress during chicken embryogenesis

city: Guangzhou

first: Yan

last: Yu

address: Huangpu street

country: China

institute: Jinan University

summary: This manuscript is about our recent work on investigating the effective mechanism of Zinc oxide Nanoparticles on the malformation of craniofacial skeleton. Briefly, we focused on addressing the phenotype of destroyed cranial neural crest cells’ development where the effect of oxidant stress was explored when developing early embryos were exposed to Zinc oxide Nanoparticles during the embryogenesis.

overall_design: mRNA profiles of early chicken embryos of control and Zinc oxide Nanoparticles-treated group, in trilicate.

first: Yu

last: Yan

first: Guang

last: Wang

first: Ju

last: Huang

last: Zhang

first: Xin

last: Cheng

first: Man

middle: l

last: Chuai

first: Beate

middle: B

last: Saberi

first: Guo

first: Xue

middle: S

last: Yang


title: RNA-seq of human HFF fibroblasts at different population doublings

first: JenAge

last: Project

summary: Gene expression of human BJ fibroblasts at different population doublings (PD) were compared. RNA-seq data comprise 2 groups: old and young HFF fibroblasts.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 4 samples: 15, 20 and 69, 72 PD

first: Peter

last: Hemmerich

first: Shiva

last: Marthandan


title: Sequencing of human HFF fibroblasts during replicative senescence (smallRNA)

type: Non-coding RNA profiling by high throughput sequencing

summary: small RNA gene expression profiles of senescent human fibroblasts were compared to young proliferating fibroblasts. RNA-seq data comprises 5 groups: 16, 26, 46, 64 and 74 population doublings of HFF fibroblasts.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 15 samples in 5 groups: 16 PD (3 samples), 26 PD (3 samples), 46 PD (3 samples), 64 PD (3 samples), 74 PD (3 samples)

first: Mario

last: Baumgart

first: Alessandro

last: Cellerino


title: RNA-seq of human BJ fibroblasts at different population doublings

summary: Comparison of gene expression of human BJ fibroblasts at different population doublings (PD). RNA-seq data comprises 2 groups: 34 and 70 population doublings of BJ fibroblasts.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 4 samples in 2 groups: 34 PD (2 samples), 70 PD (2 samples)

first: Rolf

last: Hühne


title: RNA-seq of human fibroblasts control and FLI-06 perturbation

summary: Human BJ fibroblasts were treated with FLI-06 and gene expression was compared to untreated fibroblasts. RNA-seq data comprises 2 groups: treated and untreated BJ fibroblasts.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 6 samples in two groups: control (3 samples), FLI-06 (3 samples)

first: Marco

last: Groth


title: Sequencing of Nothobranchius furzeri brain in 39 weeks old animals

summary: small RNA gene expression profiles from Nothobranchius furzeri brain of 39 weeks old animals. The RNA-seq data comprise 1 groups.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 6 samples obtained from 39 weeks old animals

first: Matthias

last: Platzer


title: Sequencing of small RNAs of human skin in different 4 age cohorts.

summary:
Comparison of temporal small RNA expression levels in skin between different human age cohorts. RNA-seq data comprise 4 age groups: 24-29 years, 45-50 years, 60-65years and 75-80 years.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design:
30 samples in 4 groups: 24-29 year (6 samples), 45-50 year (9 samples), 60-65 year (7 samples), 75-80 year (8 samples)

**Submitter declares that raw data are not provided due to donor privacy concerns**

first: Christiane

last: Frahm

first: Otto

middle: W

last: Witte

first: Madlen

last: Günther

first: Steffen

last: Priebe


title: Sequencing of Mus musculus skin of five different age groups (smallRNA)

summary: Comparison of  temporal small RNA gene expression from Mus musculus skin. The RNA-seq data comprise 5 groups at ages: 2, 9, 15, 24 and 30 months.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 25 samples in 5 groups: 2 months (5 samples), 9 months (5 samples), 15 months (5 samples), 24 months (5 samples), 30 months (5 samples)


title: Sequencing of Mus musculus brain (hemisphere) after enriched environment

summary: Comparison of gene expression profiles from Mus musculus brain (hemisphere) of animals kept in standard environment and enriched environment. The RNA-seq data comprise 4 groups: 2 age groups, each w/ and w/o enriched environment.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 24 samples in 4 groups: 5 months control (7 samples), 5 months enriched environment (5 samples), 24 months control (6 samples), 24 months enriched environment (6 samples)


title: Sequencing of Mus musculus brain (hippocampus) after enriched environment 2

summary: Comparison of gene expression profiles from Mus musculus brain of animals kept in standard environment and enriched environment. The RNA-seq data comprise 4 groups: 2 age groups, each w/ and w/o enriched environment.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 20 samples in 4 groups: 5 months control  (5 samples), 5 months enriched environment (5 samples), 24 monthscontrol (5 samples), 24 months enriched environment (5 samples)


title: Sequencing of Danio rerio brain for 5 age groups

summary: Comparison of temporal small RNA gene expression profiles from Danio rerio brain. The smallRNA-seq data comprise 5 age groups at 6, 12, 24, 36 and 42 months.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 25 samples in 5 groups: 6 month (5 samples), 12 months (5 samples), 24 months (5 samples), 36 months (5 samples), 42 months (5 samples).

first: Nils

last: Hartmann

first: Christoph

last: Englert


title: Sequencing of human MRC-5 fibroblasts at two population doublings

summary: Gene expression profiles of human fibroblasts at different population doublings were compared. RNA-seq data comprise 2 groups: 35 and 66 population doublings.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 4 samples in 2 groups: 35 PDs (2 Samples), 66 PDs (2 Samples)


title: Sequencing of human IMR-90 at 27 and 55 population doublings

summary: Comparisong of gene expression of human IMR-90 at 27 and 55 population doublings. RNA-seq data comprises 2 groups: 27 and 55 population doublings of  IMR-90.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 4 samples in 2 groups: 27 PDs (2 Samples), 55 PDs (2 Samples)


title: Sequencing of HFF and MRC-5 human fibroblast treated with BFA and FLI-06

summary: Comparing gene expression level by Illumina sequencing of fibroblasts after different treatments (BFA, FLI-06). RNA-seq data comprise 8 groups: 2 cell lines x 2 PD x control/treatment     Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 24 samples in 8 groups: HFF: 16 PDs (3 Samples), HFF: 16 PDs BFA (3 Samples), HFF: 16 PDs FLI06 (6 Samples), MRC-5: 16 PDs (3 Samples), MRC-5: 32 PDs BFA (3 Samples), MRC-5: 32 PDs FLI06 (6 Samples)


title: Sequencing of Mus musculus brain (hemispheres) of five different age groups (smallRNA)

summary: Comparison of  temporal small RNA gene expression from Mus musculus right hemisphere. The RNA-seq data comprise 5 groups at ages: 2, 9, 15, 24 and 30 months.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Mus musculus hippocampus  after physical exercise at two different ages

summary: Comparison of gene expression profiles from Mus musculus hippocampus after physical exercise (treadmill; endurance training over 4 weeks). The RNA-seq data comprise 4 groups: 2 age groups, each w/ and w/o physical exercise.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 20 samples in 4 groups: 5 months control (5 samples), 5 months physical exercise  (5 samples), 20 months control (5 samples), 20 months physical exercise (5 samples)


title: Sequencing of small RNAs of human blood in different 4 age cohorts.

summary:
Comparison of temporal small RNA expression levels in blood between different human age cohorts. RNA-seq data comprise 4 age groups: 24-29 years, 45-50 years, 60-65 years and 75-80 years.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design:
30 samples in 4 groups: 24-29 years (7 samples), 45-50 years (9 samples), 60-65 years (7 samples), 75-80 years (7 samples)

**Submitter declares that raw data are not provided due to donor privacy concerns**


title: Sequencing of Mus musculus blood of five different age groups 2

summary: Comparison of gene expression profiles from Mus musculus blood of different age groups. The RNA-seq data comprise 5 groups at ages: 2, 9, 15, 24 and 30 months.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 28 samples in 5 groups: 2 months (6 samples), 9 months (5 samples), 15 months (7 samples), 24 months (5 samples), 30 months (5 samples)


title: Sequencing of Mus musculus brain (hemispheres) of five different age groups

summary: Comparison of gene expression profiles from Mus musculus brain (hemispheres) of different age groups. The RNA-seq data comprise 5 groups at ages: 2, 9, 15, 24 and 30 months.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Nothobranchius furzeri brain in two age groups

summary: Comparison of small RNA gene expression profiles from Nothobranchius furzeri brain of 2 age groups. The RNA-seq data comprise 2 groups: 6 and 26 weeks.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 8 samples in 2 groups: 6 weeks (4 Samples), 26 weeks (4 Samples)


title: Sequencing of Mus musculus brain (hemisphere) of 5 months old animals

summary: Comparison of gene expression profiles from Mus musculus brain (hemisphere) at age 5 months following enriched environment. The RNA-seq data comprise 1 groups.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 5 samples: 5 months


title: Sequencing of Mus musculus hemisphere after physical exercise at two different ages

summary: Comparison of gene expression profiles from Mus musculus cerebral hemisphere after physical exercise (treadmill; endurance training over 4 weeks). The RNA-seq data comprise4 groups: 2 age groups, each w/ and w/o physical exercise.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 20 samples in 4 groups: 5 months control (5 samples), 5 months physical exercise (5 samples), 20 months control (5 samples), 20 months physical exercise (5 samples)


title: Sequencing of Caenorhabditis elegans at two different time points after Rotenone and DMSO treatment (smallRNA)

summary:
Comparison of small RNA expression profiles from C. elegans of Rotenone and Dimethylsulfoxid (DMSO) treated animals. The RNA-seq data comprise two age groups (5 and 15 days) and two different conditions (rotenone, DMSO).
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 12 Samples in 4 groups: 5 days DMSO (3 Samples), 5 days Rotenone (3 Samples), 15 days DMSO (3 Samples), 15 days Rotenone (3 Samples)

first: Michael

last: Ristow

first: Kim

last: Zarse


title: Sequencing of Caenorhabditis elegans at 4 different time points

summary:
small RNA gene expression profiles of C. elegans in 4 age groups. The RNA-seq data comprise 4 age groups (1, 5, 10 and 20 days after L4).
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 11 samples in 4 groups: 1 days (3 Samples), 5 days (3 Samples), 10 days (3 Samples), 20 days (2 Samples)


title: Gene expression profiling to study the influence of OP50 diet on lifespan of C. elegans.

summary:
Transcriptome profiling of C. elegans wildtype strain (N2) fed heat-inactivated OP50 diet for 5 days after L4 larvae stage.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 2 samples: wild type diet OP50


title: Sequencing of Caenorhabditis elegans at 5 different time point after Rotenone and DMSO treatment (smallRNA)

summary:
Comparison of small RNA expression profiles from C. elegans at different time points after Rotenone and Dimethylsulfoxid (DMSO) treatment. The RNA-seq data comprise 5 time points (6 hours, 1, 2, 3 and 5 days) treated with Rotenone and DMSO as well as 2 time points (3 and 5 days) with an additional H2O treatment.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 36 samples in 12 groups: 6 hour DMSO (3 Samples), 6 hour Rotenone (3 Samples), 1 day DMSO (3 Samples), 1 day H2O (3 Samples), 1 day Rotenone (3 Samples), 2 day DMSO (3 Samples), 2 day Rotenone (3 Samples), 3 days DMSO (3 Samples), 3 days Rotenone (3 Samples), 5 days DMSO (3 Samples), 5 days H2O (3 Samples), 5 days Rotenone (3 Samples)


title: Sequencing of Mus musculus muscle after physical exercise in C57BL/6 and NRF2-KO

summary:
Comparison of gene expression profiles from Mus musculus muscle after physical exercise (treadmill). The RNA-seq data comprise 4  groups: 2 strains, each w/ and w/o physical exercise.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 12 samples in 4 groups:  C57BL/6 w/o physical exercise (3 samples),  C57BL/6 w/ physical exercise (3 samples), NRF2-KO w/o physical exercise (3 samples),  NRF2-KO w/ physical exercise (3 samples)


title: Sequencing of endogenous mRNA from Caenorhabditis elegans at two time points in the presence and absence of arsenite

summary:
Background: Arsenite is one of the most toxic chemical substances known and is assumed to exert detrimental effects on viability even at lowest concentrations. By contrast and unlike higher concentrations, we here find that exposure to low-dose arsenite promotes growth of cultured mammalian cells. In the nematode C. elegans, low-dose arsenite promotes resistance against thermal and chemical stressors, and extends lifespan of this metazoan, whereas higher concentrations reduce longevity.  While arsenite causes a transient increase in reactive oxygen species (ROS) levels in C. elegans, co-exposure to ROS scavengers prevents the lifespan-extending capabilities of arsenite, indicating that transiently increased ROS levels act as transducers of arsenite effects on lifespan, a process known as mitohormesis. Worms were exposed to 100nM Arsenite 48h after L4.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 8 Samples in 4 groups: 1 day H2O (2 Samples), 1 day Arsenite (2 Samples), 5 days H2O (2 Samples), 5 days Arsenite (2 Samples)


title: Sequencing of Caenorhabditis elegans at 4 different time points after Rotenone and DMSO treatment (small RNA)

summary:
Comparison of small RNA expression profiles from C. elegans after Rotenone and Dimethylsulfoxid (DMSO) treatment. The RNA-seq data comprise 4 age groups (1, 5, 10 and 20 days) and two different treatments (Rotenone and DMSO).
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 22 samples in 8 groups: 1 days 2-Deoxyglucose (3 Samples), 1 days Rotenone (3 Samples), 5 days 2-Deoxyglucose (3 Samples), 5 days Rotenone (3 Samples), 10 days 2-Deoxyglucose (3 Samples), 10 days Rotenone (3 Samples), 20 days Rotenone (2 Samples), 20 days 2-Deoxyglucose (2 Samples)


title: Sequencing of Caenorhabditis elegans at two different time points after Rotenone and DMSO treatment (mRNA)

summary:
Comparison of gene expression profiles from C. elegans of Rotenone and Dimethylsulfoxid (DMSO) treated animals. The RNA-seq data comprise two age groups (5 and 15 days) and two different conditions (rotenone, DMSO).
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 12 samples in 4 groups: 5 days DMSO (3 Samples), 5 days Rotenone (3 Samples), 15 days DMSO (3 Samples), 15 days Rotenone (3 Samples)


title: Sequencing of Mus musculus blood of five different age groups (smallRNA)

summary: Comparison of  temporal small RNA gene expression from Mus musculus blood. The RNA-seq data comprise 5 groups at ages: 2, 9, 15, 24 and 30 months.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 25 samples in 5 groups: 2 months (5 samples), 9 months (5 samples), 15 months (5 samples), 24 months (5 samples), 30 months (5 samples)


title: Sequencing of Caenorhabditis elegans wildtype strain (N2) treated with T25B9.1 RNAi for 2 and 5 days after L4 larvae stage.

summary:
Comparison of gene expression profiles from C. elegans wildtype strain (N2) treated with L4440 and T25B9.1 RNAi for 2 days after L4 larvae stage.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 6 samples in 2 groups: N2, L4440 2 days (3 Samples); N2, T25B9.1 2 days (3 Samples)


title: Sequencing of Caenorhabditis elegans overexpression mutants.

summary:
Comparison of gene expression profiles from C. elegans mutant strains (MIR73, MIR75 or MIR77) overexpressing genes involved in proline metabolism (B0513.5 or T22H6.2) with wildtype strain (N2) at 5 days after L4 larvae stage.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 12 samples in 4 groups: N2 (3 Samples);  MIR73 (B0513.5::GFP) (3 Samples); MIR75 (B0513.5::GFP) (3 Samples); MIR77 (T22H6.2::GFP) (3 Samples)


title: Sequencing of Caenorhabditis elegans deletion mutants treated with RNAi

summary:
Comparison of gene expression profiles from C. elegans mutant strain CF1038 treated with L4440 and K02A4.1 RNAi  and C. elegans mutant strain TU3311 treated with L4440 and B0412.2 RNAi for 5 days after L4 larvae stage.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 12 samples in 4 groups: CF1038 - daf-16(mu86), bcat-1 (3 Samples); CF1038 - daf-16(mu86), L4440 (3 Samples); TU3311 (sid-1 tg; neuronal RNAi), daf-7 (3 Samples); TU3311 (sid-1 tg; neuronal RNAi), L4440 (3 Samples)


title: Sequencing of Caenorhabditis elegans treated with L4440 and 6B3B.9

summary:
Comparison of gene expression profiles from C. elegans treated with L4440 and 6B3B.9. The RNA-seq data comprise two groups.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 6 Samples in 2 groups: L4440 (3 Samples), 6B3B.9 (3 Samples)


title: Sequencing of Nothobranchius furzeri (strain: MZM-04/10p) skin after physical exercise in 2 age groups

summary:
Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-04/10p) skin for 2 age groups after physical exercise (swim-tunnel). For physical exercise, fish were placed in swim-tunnel for 4 weeks  and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 3 groups.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 20 samples in 3 groups: 9 weeks w/o physical exercise (5 Samples), 9 weeks w/ physical exercise (5 Samples), 27 weeks w/ physical exercise (10 Samples)


title: Sequencing of Nothobranchius fuzeri muscle (strain: line 4010; Tg(mylz2:egfp,tfam)) after physical exercise

summary:
Comparison of gene expression profiles from Nothobranchius furzeri  (strain: line 4010; Tg(mylz2:egfp,tfam)) muscle of animals with and without physical exercise. For physical exercise, fish were placed in swim-tunnel for 4 weeks  and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 2 groups, one with and one without physical exercise (swim-tunnel).
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 10 samples in 2 groups: w/ physical exercise (5 samples), w/o physical exercise (5 samples)


title: Sequencing of Nothobranchius furzeri (strain: MZM-04/10p) skin from Rotenone treated animals in two age groups

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-04/10p) skin for 2 age groups treated with Rotenone and DMSO. The RNA-seq data comprise 4 groups: two age groups, each treated with different Rotenone dose levels.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 20 samples in 4 groups: 9 weeks 0.1% LC50 Rotenone (5 Samples), 9 weeks 1% LC50 Rotenone (5 Samples), 9 weeks 10% LC50 Rotenone (5 Samples), 27 weeks 9 weeks 1% LC50 Rotenone (5 Samples)


title: Sequencing of Caenorhabditis elegans after 9 different RNAi treatments

summary: Comparison of gene expression profiles from C. elegans treated with 9 different RNAis. The RNA-seq data comprise 9 groups (C01A2.5, F25H2.5, F26D12.1, F55H2.6, L4440, M04C9.5, R04E5.10, R186.7, ZK795.1)    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 30 samples in 9 groups: C01A2.5 (3 Samples), F25H2.5 (3 Samples), F26D12.1 (3 Samples), F55H2.6 (3 Samples), L4440 (6 Samples), M04C9.5 (3 Samples), R04E5.10 (3 Samples), R186.7 (3 Samples), ZK795.1 (3 Samples)


title: Sequencing of Caenorhabditis elegans treated with 3 different RNAi.

summary:
Comparison of gene expression profiles from C. elegans treated with L4440,  B0395.3 and H28O16.1. The RNA-seq data comprise three groups.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 9 Samples in 3 groups: B0395.3 (3 Samples), H28O16.1 (3 Samples), L4440 (3 Samples)


title: Sequencing of Caenorhabditis elegans treated with L4440, M05B5.3 and T14F9.5 at two different time points

summary:
Comparison of gene expression profiles from C. elegans treated with L4440, M05B5.3 and T14F9.5. The RNA-seq data comprise two age groups (1 and 5 days) and 3 different RNAi treatments (L4440, M05B5.5, T14F9.5).
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 18 samples in 6 groups: 1 days L4440 (3 Samples), 1 days M05B5.5 (3 Samples), 1 days T14F9.5 (3 Samples), 5 days L4440 (3 Samples), 5 days M05B5.5 (3 Samples), 5 days T14F9.5 (3 Samples)


title: Sequencing of Nothobranchius fuzeri skin (strain: line 4010; Tg(mylz2:egfp,tfam)) after physical exercise

summary:
Comparison of gene expression profiles from Nothobranchius furzeri skin (strain: line 4010; Tg(mylz2:egfp,tfam)) of animals with and without physical exercise. For physical exercise, fish were placed in swim-tunnel for 4 weeks and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 2 groups, one with and one without physical exercise (swim-tunnel).
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of C.elegans at different time points treated with bcat-1 RNAi and controls

summary:
Comparison of gene expression profiles of C. elegans treated with bcat-1 RNAi
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 12 samples in 4 groups: 1 day L4440 (3 Samples), 1 day bcat-1 (3 Samples), 2 days L4440 (3 Samples), 2 days bcat-1 (3 Samples)


title: Sequencing of Nothobranchius furzeri (strain: MZM-04/10p) liver after physical exercise in 2 age groups

summary:
Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-04/10p) liver for 2 age groups after physical exercise (swim-tunnel). For physical exercise, fish were placed in swim-tunnel for 4 weeks and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s).The RNA-seq data comprise 3 groups.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Caenorhabditis elegans at 5 different time point after Rotenone and DMSO treatment (mRNA)

summary:
Comparison of gene expression profiles from C. elegans at different time points after Rotenone and Dimethylsulfoxid (DMSO) treatment. The RNA-seq data comprise 5 time points (6 hours, 1, 2, 3 and 5 days) treated with Rotenone and DMSO as well as 2 time points (3 and 5 days) with an additional H2O treatment.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 36 samples in 12 groups: 6 hours DMSO (3 Samples), 6 hours Rotenone (3 Samples), 1 day DMSO (3 Samples), 1 day H2O (3 Samples), 1 day Rotenone (3 Samples), 2 day DMSO (3 Samples), 2 day Rotenone (3 Samples), 3 days DMSO (3 Samples), 3 days Rotenone (3 Samples), 5 days DMSO (3 Samples), 5 days H2O (3 Samples), 5 days Rotenone (3 Samples)


title: Sequencing of Nothobranchius furzeri (strain: MZM-04/10p) brain after physical exercise in 2 age groups

summary:
Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-04/10p) brain for 2 age groups after physical exercise (swim-tunnel). For physical exercise, fish were placed in swim-tunnel for 4 weeks and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 3 groups.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Nothobranchius fuzeri (strain: GRZ) skin after physical exercise

summary:
Comparison of gene expression profiles from Nothobranchius furzeri (strain: GRZ) skin after physical exercise. For physical exercise, fish were placed in swim-tunnel for 4 weeks  and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 10 samples.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 10 samples w/ physical exercise


title: Sequencing of Nothobranchius furzeri liver (strain: MZM-04/10p) from Rotenone treated animals in two age groups

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-04/10p) liver for 2 age groups treated with Rotenone and DMSO. The RNA-seq data comprise 4 groups: two age groups, each treated with different Rotenone dose levels.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 20 samples in 4 groups: 9 weeks 0.1% LC50 Rotenone (5 Samples), 9 weeks 1% LC50 Rotenone (5 Samples), 9 weeks 10% LC50 Rotenone (5 Samples), 27 weeks 1% LC50 Rotenone (5 Samples)


title: Sequencing of Nothobranchius furzeri (strain: MZM-04/10p) brain from Rotenone and DMSO treated animals in two age groups

summary: Comparison of gene expression profiles from Nothobranchius furzeri brain (strain: MZM-04/10p) for 2 age groups treated with Rotenone and Dimethylsulfoxid (DMSO). The RNA-seq data comprise 2 x 2 groups: two age groups (9, 27 weeks), each treated with Rotenone and DMSO.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 20 samples in 2 x 2 groups: 9 weeks w/ DMSO (5 Samples), 9 weeks w/ 1% LC50 Rotenone (5 Samples), 27 weeks w/ DMSO (5 Samples), 27 weeks w/ 1% LC50 Rotenone (5 Samples)


title: Sequencing of Nothobranchius fuzeri (strain: GRZ) brain after physical exercise

summary:
Comparison of gene expression profiles from Nothobranchius furzeri (strain: GRZ) brain after physical exercise. For physical exercise, fish were placed in swim-tunnel for 4 weeks and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 10 samples.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Danio rerio embryo from wildtype and microRNA treated animals

summary:
Comparison of gene expression profiles from Danio rerio embryos of wiltype, miR-101a and miR-29a treated animals. The RNA-seq data comprise 3 groups.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 12 samples in 3 groups: wildtype (4 samples), miR-101a (4 samples), miR-29a (4 samples)

first: Aurora

last: Savino


title: Sequencing of Nothobranchius fuzeri (strain: GRZ) liver after physical exercise

first: JenAge

last: Project

summary:
Comparison of gene expression profiles from Nothobranchius furzeri (strain: GRZ) liver after physical exercise. For physical exercise, fish were placed in swim-tunnel for 4 weeks  and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 10 samples.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Nothobranchius furzeri  (strain: MZM-04/10p) brain from Rotenone treated animals in two age groups

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-04/10p) brain for 2 age groups treated with Rotenone and DMSO. The RNA-seq data comprise 4 groups: two age groups, each treated with different Rotenone dose levels. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Nothobranchius furzeri (strain: MZM-0410p) skin after Rotenone and DMSO treatment

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-0410p) skin of Rotenone and Dimethylsulfoxid (DMSO) treated animals. The RNA-seq data comprise 2 groups.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 10 samples in 2 groups: DMSO (5 samples), Rotenon 15pM (5 samples)


title: Sequencing of Nothobranchius fuzeri (strain: line 4010; Tg(mylz2:egfp,tfam)) brain after physical exercise

summary:
Comparison of gene expression profiles from Nothobranchius furzeri  (strain: line 4010; Tg(mylz2:egfp,tfam)) brain of animals with and without physical exercise. For physical exercise, fish were placed in swim-tunnel for 4 weeks and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 2 groups, one with and one without physical exercise (swim-tunnel).
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Nothobranchius fuzeri (strain: line 4010; Tg(mylz2:egfp,tfam)) liver after physical exercise

summary:
Comparison of gene expression profiles from Nothobranchius furzeri (strain: line 4010; Tg(mylz2:egfp,tfam)) liver of animals with and without physical exercise. For physical exercise, fish were placed in swim-tunnel for 4 weeks  and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 2 groups, one with and one without physical exercise (swim-tunnel).
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Nothobranchius fuzeri muscle (strain: GRZ) after physical exercise

summary:
Comparison of gene expression profiles from Nothobranchius furzeri  (strain: GRZ) muscle after physical exercise. For physical exercise, fish were placed in swim-tunnel for 4 weeks and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 10 samples.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Nothobranchius furzeri (strain: GRZ) liver from Rotenone treated animals

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: GRZ) liver of Rotenone and Dimethylsulfoxid (DMSO) treated animals. The RNA-seq data comprise 3 groups: one control group (DMSO) and two groups with different Rotenone dose levels.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 15 samples in 3 groups: DMSO (5 Samples), 15pM Rotenone (5 Samples), 150pM Rotenone (5 Samples)


title: Sequencing of Nothobranchius furzeri (strain: GRZ) liver in different age groups

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: GRZ) liver of different age groups. The RNA-seq data comprise 4 groups: 5, 7, 10, and 14 weeks.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 20 samples in 4 groups: 5 weeks (5 Samples), 7 weeks (5 Samples), 10 weeks (5 Samples), 14 weeks (5 Samples)


title: Sequencing of Danio rerio brain from wildtype and Tg-microRNA-sponge animals

summary:
Comparison of gene expression profiles from Danio rerio brain of wiltype and  Tg-microRNA-sponge animals. The RNA-seq data comprise 3 groups.

Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 12 samples in 3 groups: wildtype (4 samples), actb1::miR-29sponge (4 samples), kif5a::miR-29sponge (4 samples)

first: Roberto

last: Ripa


title: Sequencing of Nothobranchius furzeri (strain: GRZ) brain in different age groups

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: GRZ) brain of different age groups. The RNA-seq data comprise 4 groups: 5, 7, 10, and 14 weeks.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Nothobranchius furzeri (strain: GRZ) brain from Rotenone treated animals

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: GRZ) brain of Rotenone and Dimethylsulfoxid (DMSO) treated animals. The RNA-seq data comprise 3 groups: one control group (DMSO) and two groups with different Rotenone dose levels.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Nothobranchius furzeri (strain: GRZ) skin from Rotenone treated animals

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: GRZ) skin of Rotenone and Dimethylsulfoxid (DMSO) treated animals. The RNA-seq data comprise 3 groups: one control group (DMSO) and two groups with different Rotenone dose levels.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Nothobranchius furzeri (strain: MZM-04/10p) muscle after physical exercise in 2 age groups

summary:
Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-04/10p) muscle for 2 age groups after physical exercise (swim-tunnel). For physical exercise, fish were placed in swim-tunnel for 4 weeks and were swimming 6 times per day for 5 min duration (water velocity 14 cm/s). The RNA-seq data comprise 3 groups.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Nothobranchius furzeri (strain: MZM-0410p) brain from microRNA treated animals 1

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-0410p) brain of miRNA treated animals (scrambled control, antagomiR101a). The RNA-seq data comprise 2 groups.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 10 samples in 2 groups: scrambled control (5 samples), antagomiR-101a (5 samples)


title: Sequencing of Nothobranchius furzeri (strain: GRZ) skin in different age groups

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: GRZ) skin of different age groups. The RNA-seq data comprise 4 groups: 5, 7, 10, and 14 weeks.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Danio rerio skin for 2 age groups after physical exercise

summary:
Comparison of gene expression profiles from Danio rerio skin for 2 age groups. The RNA-seq data comprise 2 x 2 groups: two age groups, each with and without physical exercise (swim-tunnel).
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise (5 samples), 1 year w/o physical exercise (5 samples), 3 year w/ physical exercise (5 samples), 3 year w/o physical exercise (5 samples)


title: Sequencing of Danio rerio liver from tert mutants and controls

summary:
Comparison of gene expression profiles from Danio rerio liver of wiltype (AB) and homozygote/heterozygote tert mutants (AB tert(-/-), AB tert(+/)). The RNA-seq data comprise 3 groups.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 13 samples in 3 groups: AB (5 samples), AB tert(-/-) (3 samples), AB tert(+/-) (5 samples)


title: Sequencing of Danio rerio liver for 2 age groups after physical exercise

summary:
Comparison of gene expression profiles from Danio rerio liver for 2 age groups. The RNA-seq data comprise 2 x 2 groups: two age groups, each with and without physical exercise (swim-tunnel).
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 20 samples in 2 x 2  groups: 1 year w/ physical execrise (5 samples), 1 year w/o physical exercise (5 samples), 3 year w/ physical exercise (5 samples), 3 year w/o physical exercise (5 samples)


title: Sequencing of Danio rerio muscle for 2 age groups after physical exercise

summary:
Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA-seq data comprise 2 x 2 groups: two age groups, each with and without physical exercise (swim-tunnel).
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Nothobranchius furzeri (strain: MZM-0410p) liver after Rotenone and DMSO treatment

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-0410p) liver of Rotenone and Dimethylsulfoxid (DMSO) treated animals. The RNA-seq data comprise 2 groups.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Expression data from Acinetobacter baumannii planktonic, biofilm, and antibiotic treated biofilm samples

status: Public on Oct 18 2021

city: Bozeman

first: Kerry

last: Williamson

state: Montana

address: 109 Lewis Hall

department: Microbiology and Immunology

country: USA

institute: Montana State University

summary:
Is there a universal genetically programmed defense providing tolerance to antibiotics when bacteria grow as biofilms?   A comparison between biofilms of three different bacterial species by transcriptomic and metabolomic approaches uncovered no evidence of one. Single-species biofilms of three bacterial species (Pseudomonas aeruginosa, Staphylococcus aureus, and Acinetobacter baumannii) were grown in vitro for three days then challenged with respective antibiotics (ciprofloxacin, daptomycin, tigecycline) for an additional 24 h. All three microorganisms displayed reduced susceptibility in biofilms compared to planktonic cultures. Global transcriptomic profiling of gene expression comparing biofilm to planktonic and antibiotic-treated biofilm to untreated biofilm was performed.  Extracellular metabolites including 18 amino acids, glucose, lactate, acetate, formate, and ethanol were measured to characterize the utilization of carbon sources between biofilms, treated biofilms, and planktonic cells. While all three bacteria exhibited a species-specific signature of stationary phase, no conserved gene, gene set, or common functional pathway could be identified that changed consistently across the three microorganisms. Across the three species, glucose consumption was increased in biofilms compared to planktonic cells and alanine and aspartic acid utilization were decreased in biofilms compared to planktonic cells.  The reasons for these changes were not readily apparent in the transcriptomes. No common shift in the utilization pattern of carbon sources was discerned when comparing untreated to antibiotic-exposed biofilms. Overall, our measurements do not support the existence of a common genetic or biochemical basis for biofilm tolerance against antibiotics. Rather, there are likely myriad genes, proteins, and metabolic pathways that influence the physiological state of microorganisms in biofilms contributing to antibiotic tolerance.
The Acinetobacter baumannii microarray data from the study described above is deposited here.

overall_design: 4 independent biological replicates were performed with plankonic, biofilm, and antibiotic treated biofilm samples. Planktonic samples were compared to biofilm samples to identify genes signficantly up- or down-regulated in biofilms. Biofilm samples were compared to antibiotic treated biofilms to indentify genes significantly up- or down-regulated by antibiotic treatment in biofilms.

first: Philip

last: Stewart

first: Laura

last: Boegli

first: Timothy

last: Hamerly

first: Ben

last: White

first: Liam

last: Scott

first: Xiao

last: Hu

first: Brendan

middle: M

last: Mumey

middle: J

last: Franklin

first: Brian

last: Bothner

first: Francisco

middle: G

last: Vital-Lopez

first: Anders

last: Wallqvist

first: Garth

middle: A

last: James


title: Sequencing of Nothobranchius furzeri (strain: MZM-0410p) brain from microRNA treated animals 2

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-0410p) brain of miRNA treated animals (scrambled control, antagomiR29a). The RNA-seq data comprise 2 groups.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 10 samples in 2 groups: scrambled control (5 samples), antagomiR-29a (5 samples)

first: Mario

last: Baumgart

first: Alessandro

last: Cellerino

first: Rolf

last: Hühne

first: Marco

last: Groth

first: Matthias

last: Platzer


title: Sequencing of Nothobranchius furzeri (strain: MZM-0410p) brain after Rotenone and DMSO treatment

first: JenAge

last: Project

summary: Comparison of gene expression profiles from Nothobranchius furzeri (strain: MZM-0410p) brain of Rotenone and Dimethylsulfoxid (DMSO) treated animals. The RNA-seq data comprise 2 groups.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Search for a Shared Genetic or Biochemical Basis for Biofilm Tolerance to Antibiotics across Bacterial Species

first: Kerry

last: Williamson

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Pseudomonas aeruginosa
Staphylococcus aureus
Acinetobacter baumannii AB5075

overall_design: Refer to individual Series


title: RNA-seq-based transcriptome analysis of a cefquinome-treated, highly resistant, and virulent MRSA strain

city: Shenzhen

first: ZAHID

last: IQBAL

address: Shenzhen University, Xili campus, A1-108

institute: Shenzhen University

summary: Cefquinome is a fourth-generation cephalosporin developed specifically for veterinary use. The mechanism of MRSA resistance to cefquinome is still not established. Therefore, we designed this study to evaluate the effect of cefquinome on the transcriptome of MRSA1679a, a strain that was isolated from a chicken. The transcriptome analysis indicated that multiple efflux pumps (QacA, NorB, Bcr, and ABCb) were upregulated in MRSA1679a as a resistance mechanism to expel cefquinome. Additionally, penicillin-binding protein 1A was overexpressed, which conferred resistance to cefquinome, a β-lactam antibiotic. Adhesion and the biofilm-forming capacity of the MRSA strain was also enhanced in addition to overexpression of many stress-related genes. Genes related to carbohydrate metabolism, secretion systems, and transport activity were also significantly increased in MRSA1679a. In conclusion, global transcription was triggered to overcome the stress induced by cefquinome, and the MRSA1679a showed a great genetic potential to survive in this challenging environment. This study provides a profound understanding of MRSA1679a as a potentially important pathogen and identifies key resistance characteristics of MRSA against cefquinome.

overall_design: Four samples were analysed including 2 cefquinome treated MRSA1679a strains and 2 untreated control MRSA1679a strains with two replicates of each.

first: Zahid

last: Iqbal

first: Haﬁz

middle: I

last: Hussain

first: Awais

last: Ihsan

first: Haihong

last: Hao


title: Sequencing of Danio rerio skin from wildtype and two tert mutant phenotypes  (JenAge)

summary:
Comparison of gene expression profiles from Danio rerio skin of wiltype (AB) and homozygote/heterozygote tert mutant phenotypes (AB tert(-/-), AB tert(+/)). The RNA-seq data comprises 3 groups.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: Overall Design: 13 samples in 3 groups: AB (5 samples), AB tert(-/-) (3 samples), AB tert(+/-) (5 samples)

first: Nils

last: Hartmann

first: Christoph

last: Englert


title: Sequencing of Danio rerio muscle from tert mutants and controls

summary:
Comparison of gene expression profiles from Danio rerio muscle of wiltype (AB) and homozygote/heterozygote tert mutants (AB tert(-/-), AB tert(+/)). The RNA-seq data comprise 3 groups.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: Sequencing of Danio rerio brain for 2 age groups after physical exercise

summary:
Comparison of gene expression profiles from Danio rerio brain for 2 age groups. The RNA-seq data comprise 2 x 2 groups: two age groups, each with and without physical exercise (swim-tunnel).
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)


title: transcriptome of storage and basal clove of garlic bulbs

status: Public on Oct 17 2021

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

summary: The garlic landrace of ‘Chalingzipisuan’ was used for transcriptome analysis. The axillary bud of garlic is at the base of clove, whereas the storage leaf at the upper clove provides essential nutrition for the germination and seedling growth. Therefore, the basal and storage clove were ere separately performed for RNA sequencing from the bulbs under three different developmental stages (i.e., enlarging growth, dormancy, and germination), generating in total 77-85 million reads.

overall_design: The basal and storage clove collected from three developmental stages were separately performed for RNA sequencing. Three biological replicates of each treatment were used. Therefore, a total of 18 samples were performed for RNA sequencing.


title: Sequencing of Danio rerio skin for 2 age groups

summary: Comparison of Danio rerio skin for 2 age groups treated with Rotenone. The RNA-seq data comprises two age groups treated with different Rotenone dose levels.    Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 26 samples in 3 groups: 1 year w/ Rotenone 3.75nM (9 samples), 1 year w/ Rotenone 37.5nM (9 samples), 3 year w/ Rotenone 37.5nM (8 samples).


title: Glioblastoma Stem Cells Reprogram Chromatin In Vivo To Generate Selective Therapeutic Dependencies [ChIP-Seq]

city: La Jolla

first: Deobrat

last: Dixit

address: 10901 N Torrey Pines Rd,

institute: Sanford Burnham Prebys Medical Discovery Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Glioblastomas are universally fatal cancers that contain self-renewing glioblastoma stem cells (GSCs) that initiate tumors. Traditional anti-cancer drug discovery based on in vitro cultures tends to identify targets with poor therapeutic index and fails to accurately model the effects of the tumor microenvironment. Here, leveraging in vivo genetic screening, we identified the H3K4me3 regulator DPY30 as an in vivo-specific glioblastoma dependency. Based on the hypothesis that in vivo epigenetic regulation may define critical GSC dependencies, we interrogated active chromatin landscapes of GSCs derived from intracranial xenografts and cell culture through Histone H3 lysine 4 trimethylation (H3K4me3) chromatin immunoprecipitation and transcriptome analysis. Intracranial-specific genes marked by H3K4me3 included FOS, NFkB, and phosphodiesterase family members. In intracranial tumors, DPY30 regulated angiogenesis and hypoxia pathways in an H3K4me3-dependent manner, but was dispensable in cultured GSCs. PDE4B was a key downstream effector of DPY30; the PDE4 inhibitor, rolipram, preferentially targeted DPY30-expressing cells and impaired in vivo glioblastoma growth without affecting cultured tumor cells. Collectively, DPY30 selectively regulates H3K4me3 modification on genes critical to support angiogenesis and tumor growth in vivo, laying the foundation for the DPY30-PDE4B axis as a specific and novel therapeutic target in glioblastoma with a broad therapeutic index.

overall_design: H3K4me3 ChIP was performed in 5 glioblastoma stem cell (GSC) lines grown either in cell culture or in immunocompromised mice for 3 weeks

first: Briana

last: Prager

first: Ryan

last: Gimple

first: Jeremy

last: Rich


title: E-protein inhibition in ILC2 development shapes the function of mature ILC2s during allergic airway inflammation

city: Seattle

first: Elia

middle: D.

last: Tait Wojno

state: WA

address: 750 Republican St.

department: Department of Immunology

institute: University of Washington

summary: E-protein transcription factors (TFs) limit group 2 innate lymphoid cell (ILC2) development while promoting T cell differentiation from common lymphoid progenitors (CLPs). Inhibitors of DNA-binding (Id) proteins block E-protein DNA binding in CLPs to allow ILC2 development. However, whether E-proteins influence ILC2 function upon maturity and activation remains unclear. Mice that overexpress Id1 under control of the thymus-restricted proximal Lck promoter (Id1tg/WT) have a large pool of primarily thymus-derived ILC2s in the periphery that develop in the absence of E-protein activity. We used these mice to investigate how the absence of E-protein activity affects ILC2 function and genomic landscape in response to house dust mite (HDM) allergens. Id1tg/WT mice had increased Klrg1- ILC2s in the lung compared to wild type (WT, Id1WT/WT) mice in response to HDM, but Id1tg/WT ILC2s had an impaired capacity to produce type 2 cytokines. Analysis of WT ILC2 accessible chromatin suggested that AP-1 and C/EBP TFs but not E-proteins were associated with ILC2 inflammatory gene programs. Instead, E-protein binding sites were enriched at functional genes in ILC2s during development that were later dynamically regulated in allergic lung inflammation, including genes that control ILC2 response to cytokines and interactions with T cells. Finally, ILC2s from Id1tg/WT compared to WT mice had fewer regions of open chromatin near functional genes that were enriched for AP-1 factor binding sites following HDM treatment. These data show that E-proteins shape the chromatin landscape during ILC2 development to dictate the functional capacity of mature ILC2s during allergic inflammation in the lung.

overall_design:
Accesibility profiles by ATAC-seq for ILC2 and T-cells from WT mice lungs and for ILC2 from both WT and Id1tg mice lungs, in response to IN administration of house dust mite (HDM).

Additional grant information for this study: 1DP2 OD024087

first: Gilad

last: Barshad

first: Lauren

last: Webb

first: Charles

last: Danko

middle: D


title: Glioblastoma Stem Cells Reprogram Chromatin In Vivo To Generate Selective Therapeutic Dependencies [RNA-Seq]

overall_design: RNA sequencing on 3565 and 1919 GSCs transduced with either control (nt) or DPY30 shRNA, grown either in cell culture or in immunocompromised mice for 3 weeks


title: Stat5b inhibition blocks proliferation and tumorigenicity of glioblastoma stem cells derived from a de novo murine brain cancer model

city: kyoto

first: Chiami

last: Moyama

address: Misasagi-Nakauchicho 5, Yamashina-ku

country: Japan

institute: Kyoto Pharmaceutical University

summary: Glioblastoma (GBM) is the most common and malignant type of brain cancer in adults with poor prognosis. GBM stem cells (GSCs) reside within niches in GBM tissues and contributes to recurrence and therapy resistance. Previous studies have shown that expression of leucine-rich repeat-containing G-protein coupled receptor 5 (Lgr5), a Wnt pathway-related stem cell marker, correlates with a poor prognosis in GBM, and its knockdown in GSCs induces apoptosis accompanied with downregulation of signal transducer and activator of transcription 5b (Stat5b). Here, we show that Stat5b co-localizes with Lgr5 in hypoxia-inducible factor 2α (Hif2α)-positive regions in GBM tissues. Functional analyses using GSCs derived from a murine de novo GBM model induced by oncogenic genes transduction using the Sleeping-Beauty transposon system revealed that expression of Stat5b was induced by culturing under hypoxia together with Lgr5, repressed by Hif2α knockdown, and reduced by Lgr5 knockdown or a Wnt/β-catenin signaling inhibitor ICG-001 treatment. Stat5b inhibition in the GSCs induced apoptosis and caused downregulation of Cyclin E2 resulted in blockade of entry into S-phase in the cell cycle. Disruption of Stat5b in an orthotopic transplantation model significantly prolongs event-free survival. These results suggest that Stat5b, regulated by hypoxia and the Wnt pathway, plays an important role in the maintenance and tumorigenicity of GSCs and may be a promising therapeutic molecular target to attack GSCs.

overall_design: To test the effect of suppression of Stat5b on the gene expression, murine GSC was tranducted with lentiviral non-target (control) or Stat5b shRNA. Stat5b-knockdown GSCs were compared to control cells.

first: Mitsugu

last: Fujita

first: Shota

last: Ando

first: Keiko

last: Taniguchi

first: Hiromi

last: Ii

first: Seisuke

last: Tanigawa

first: Naoya

last: Hashimoto

first: Susumu

last: Nakata


title: Sequencing of Danio rerio brain from tert mutants and controls

first: JenAge

last: Project

summary:
Comparison of gene expression profiles from Danio rerio brain of wiltype (AB) and homozygote/heterozygote tert mutants (AB tert(-/-), AB tert(+/-)). The RNA-seq data comprise 3 groups.
Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

first: Nils

last: Hartmann

first: Christoph

last: Englert

first: Rolf

last: Hühne

first: Marco

last: Groth

first: Matthias

last: Platzer


title: Sequencing of Danio rerio liver for 2 age groups

summary: Comparison of Danio rerio liver for 2 age groups treated with Rotenone. The RNA-seq data comprisess two age groups treated with Rotenone.     Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 24 samples in 3  groups: 1 year w/ Rotenone 3.75nM (9 samples), 1 year w/ Rotenone 37.5nM (9 samples), 3 year w/ Rotenone 37.5nM (6 samples).


title: the mechanism of lncRNA HOXC-AS3 in regulating brest cancer progression.

city: Jinan City

first: Wenjie

last: Zhu

state: Shangdong Province

address: Wen Hua Xi Road 44

department: Department of Pathology

institute: School of Basic Medical Sciences, Shandong University

summary: Here we show that lncRNA HOXC-AS3, a key factor in promoting brest cancer progression through metabolic reprogramming pathways.

overall_design: RNA-sequencing of HOXC-AS3-associated mRNAs in PCDNA3.1 and HOXC-AS3-overexpression 231 cells

first: Z

last: Wenjie

first: G

last: Peng


title: Sequencing of Danio rerio brain for 2 age groups after Rotenone treatment

summary: Comparison of Danio rerio brain for 2 age groups treated with Rotenone. The RNA-seq data comprises two age groups treated with different Rotenone dose levels.      Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)

overall_design: 26 samples in 3 groups: 1 year w/ Rotenone 3.75nM (10 samples), 1 year w/ Rotenone 37.5nM (9 samples), 3 year w/ Rotenone 37.5nM (7 samples).


title: Expeditious recruitment of circulating memory CD8 T cells to the liver facilitates control of malaria

city: Iowa City

first: Isaac

last: Jensen

state: IA

institute: University of Iowa

summary: Determine transcriptional changes in the mouse liver after infection with Plasmodium berghei ANKA (Pb) sporozoites

overall_design: CB6F1 mice that were unvaccinated or vaccinated with attenuated Pb sporozoites were subsequently challenged with virulent Pb sporozoites. Whole liver tissue was harvested 6 hours post infection for RNA-sequencing.

first: John

middle: T

last: Harty

first: Mitchell

middle: N

last: Lefebvre


title: MIR100HG regulates CALD1 gene expression by targeting miR-142-5p to affect the progress of bladder cancer cells in vitro revealed by long noncoding RNA sequencing (lncRNA and mRNA)

city: shanghai

first: sheng

last: zhang

address: 270 Dongan Road, Shanghai

institute: Shanghai Cancer Center, Fudan University

summary: This project completed the transcriptome analysis of 6 samples and obtained 79.158 Gb Clean Data (after quality control sequencing data). The average clean data volume of each sample was 13.193 Gb, the Q30 base percentage was over 93.02%, and the GC content was 39.35. % To 46.16%. through lncRNA sequencing, bioinformatics analysis and cell function studies, we found that MIR100HG is a new bladder cancer promoter that regulates the expression of CALD1 gene by targeting miR-142-5p and promotes the proliferation, migration and invasion of bladder cancer cells. These findings provide a new perspective for the study of the pathogenesis and development of bladder cancer, and have the potential as a new target for the diagnosis, prognosis and targeted therapy of bladder cancer.

overall_design: LncRNA profiles of 3 bladder cancer samples and 3 adjacent tissue samples

first: Sheng

last: Zhang

first: Qin

last: Wang

first: Wenfeng

last: Li

first: Jinzhong

last: Chen


title: Nicotinamide N-methyltransferase is related to MELF pattern invasion in endometrioid carcinoma [RNA-seq]

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: In endometrioid carcinoma (EC), grade 1 (G1) EC is generally associated with a good prognosis. However, in a minority of G1, we often find a more aggressive histological pattern: MELF (microcystic, elongated, and fragmented) pattern. We previously revealed that EC with high expression of S100A4 and serum deprivation-response protein (SDPR) was related to MELF pattern invasion. However, the molecular feature of the invasive front area of MELF pattern has not been investigated. In the current study, we searched for genes preferentially expressed in the invasive front area of EC with MELF pattern by using laser microdissection and RNA sequencing, and revealed that Nicotinamide N-methyltransferase (NNMT) is related to invasiveness of MELF pattern. We confirmed that NNMT expression was high in the invasive front area of MELF pattern in immunohistochemical analysis. Moreover, using endometrioid carcinoma cell lines, we showed that NNMT promotes migration, invasion, colony formation, epithelial-mesenchymal transition (EMT), and chemoresistance. We speculated that depletion of NNMT promotes histone methylation and leads to tumor suppression because NNMT consumes S-adenosyl methionine (SAM), which is an essential methylation cofactor. We showed that NNMT-knockout cells the expression of H3K9me2 was enhanced. We speculate that methylation of H3K9 lead to repress the transcription of various oncogenic genes by performing RNA sequencing using NNMT-knockout cell lines. Our findings showed the possibility that NNMT inhibitors, which are expected to be used for the treatment of metabolic disorders, is effective for the treatment of an aggressive EC. This is the first report of the gene analysis focused on the morphological changes of MELF pattern invasion of EC.

overall_design: To compare the levels of gene expression profiles between NNMT-knockout AN3CA cells and control cells, total RNA was extracted from KO1, KO2, and EV cells.

first: Shinichiro

last: Tahara

first: Eiichi

last: Morii


title: Using RNA sequencing to identify key microRNAs and hub genes in the progression of hepatocellular carcinoma

city: zhongshan

first: yongyan

last: pei

address: Long life water, wuguishan street, zhongshan city

department: School of Pharmaceutical and Chemical Engineering

institute: Guangdong Pharmaceutical University

summary: This project completed the transcriptome analysis of 6 samples and obtained 12142010 reads Clean Data (after quality control sequencing data). The average clean data volume of each sample was 1833443535 bp , the Q30 base percentage was over 80%, and the GC content was 68.15. % To 46.53%. In this study, we used RNA sequencing and integrated bioinformatics approach to explore hub miRNA-mRNA interactions that are highly associated with hepatocellular carcinoma development. Our data indicated that miR-139-5p is closely related to the overall survival rate of hepatocellular carcinoma patients and directly combines with ITGB8 to regulate its expression.

overall_design: miRNA profiles of 3 hepatocellular carcinoma samples and 3 adjacent tissue samples

first: Nana

last: Miao

first: Yunfei

last: Niu

first: Wei

last: Wei

first: Yulong

last: Dong

first: Chenjie

last: Tao

first: Lieping

last: Guo

first: Yongyan

last: Pei


title: Quantitive analysis of transcriptome alteration after treatment with J007(a hnrnp A1 inhibitor) in murine myeloma  cells

city: Los Angeles

first: Yijiang

last: Shi

address: 11301 wilshire blvd

institute: UCLA

summary:
Purpose: To perform an unbiased evaluation of altered gene expression in J007 treated MM cells.
Methods:mRNA profiles in myc-driven murine myeloma cells both before and after J007 treatment were generated by Illumina HiSeq 3000 sequencer. The differential gene expressions were examined using DESeq2 algorithm.  QIAGEN Ingenuity Pathway Analysis (IPA) software was used for pathway enrichment analysis of differentially expressed genes.
Results: 257 genes that were upregulated greater than 2x fold and 230 genes that were downregulated at least 50% by J007.  The most significantly altered gene set was that of ‘myc targets.  The ‘angiogenesis’, ‘mTORC1 signaling’, ‘protein secretion’, ‘G2M checkpoint’, ‘unfolded protein response’ and ‘fatty acid metabolism’ gene sets were also decreased by J007 .
Conclusion: The results support that J007 functions as expected to inhibit hnrnpa1 and  c-myc binding in vivo.

overall_design: Comparison of mRNA profiles before and after J007 treatment

first: Fumou

last: Sun

first: Yan

last: Cheng

first: Brent

last: Holmes

first: Binod

last: Dhakal

first: Joseph

last: Gera

first: Siegfried

last: Janz

first: Alan

last: Lichtenstein


title: Transcriptome of in vitro fertilized 7-day-old bovine blastocysts

city: Ithaca

first: Vimal

last: Selvaraj

state: NY

address: 204 Morrison Hall

department: Animal Sciences

institute: Cornell University

summary: Blastocysts consist of cells that form the inner cell mass and the trophectoderm. The full transcriptome of bovine blastocyst embryos was examined in this study. Total RNA was isolated from three independent batches of blastocysts. Using Poly(A) capture mRNA was isolated and cDNA libraries prepared using Illumina TruSeq RNA sample Prep Kit. The libraries were sequenced using Illumina HiSeq 4000. This dataset should serve as a baseline for understanding bovine pluripotency and trophoblast stem cells providing a snapshot for functional interpretation of preimplantation embryo development.

overall_design: Baseline gene expression in bovine blastocysts.

first: Viju

middle: V

last: Pillai

first: Prasanthi

middle: P

last: Koganti


title: Stimulations of the growth rate in elevated CO2 condition were observed in over-expression or RNA interference lines of genes identified by intraspecific variation analyses.

status: Public on Oct 16 2021

city: Iizuka

first: Kousuke

last: Hanada

state: Fukuoka

address: 680-4 Kawazu

department: Department of Bioscience and Bioinformatics

institute: Kyushu Institute Technology

summary: In the present study, we sought genes that are involved in the variation of the enhancement of plant growth rate among the Arabidopsis thaliana ecotypes in elevated CO2 condition. We performed a combination analysis of a genome wide association study (GWAS), and a transcriptome study to seek the candidate genes. GWAS was performed using the growth analysis data obtained at Oguchi et al. and the whole genome data from 31 ecotypes. The transcriptome analysis was performed for 6 ecotypes that had contrasting CO2 responses in the growth rate. We analyzed not only annotated coding genes but also small coding genes (30–100 amino acids) identified by Hanada et al., most of which were shown to play roles in cell-to-cell signaling, because it has been shown that a number of small coding genes play significant roles in environmental responses. We also studied the effect of the altered expression of the candidate genes on the plant growth rate in elevated CO2 condition using over-expression (OX) transgenics and RNA interference (RNAi) transgenics. We show that transgenic plants of three genes had significantly higher growth rate under the elevated CO2 condition.

overall_design: For the microarray analysis, we selected 3 ecotypes that showed a bigger enhancement of growth rate under the elevated CO2 condition (Bur-0, Fei-1 and Sf-1), and 3 ecotypes that showed a smaller enhancement of growth rate under the elevated CO2 condition (Col-0, Te-0 and Yeg-1) according to our growth analysis


title: High-throughput sequencing approach for the identification of lncRNA biomarkers in hepatocellular carcinoma and reveal the effect of ZFAS1 on hepatocellular carcinoma progression（lncRNA and mRNA）

first: yongyan

last: pei

summary: The aim of this study was to screen abnormal lncRNAs in the progression of hepatocellular carcinoma through high-throughput sequencing, and to screen the biomarkers for prognosis and diagnosis of hepatocellular carcinoma. Transcriptome analysis of 6 samples was completed in this project. A total of 93.581 Gb Clean Data (sequencing Data after quality control) was obtained. The average amount of Clean Data of each sample was 15.597 Gb. The Q30 base percentage was above 93.69 % and GC content was between 44.95% and 50.05%. In conclusion, sequencing analysis provided a landscape for abnormal regulation of lncRNAs, and screened out a significantly different lncRNAs ZFAS1. ZFAS1were found to be overexpressed in hepatocellular carcinoma tissues and correlated with malignant status and prognosis of hepatocellular carcinoma patients, and ZFAS1 silencing inhibited proliferation, migration and invasion of SK-Hep1 cells. The overexpression of miR-582-3p can eliminate the inhibitory effect of ZFAS1 silencing on SK-Hep1 cells, which may be valuable for the diagnosis and treatment of hepatocellular carcinoma. ZFAS1 may be a new potential biomarker for liver cancer. Further studies on the regulatory process of ZFAS1/miR-582-3p will help us to understand the mechanism of the occurrence and development of liver cancer

overall_design: LncRNA profiles of 3 hepatocellular carcinoma samples and 3 adjacent tissue samples

first: Peng

last: Zhu

first: Jian

last: Yu

first: Wenbin

last: Ding

first: Yun

last: Yang

first: Fuchen

last: Liu

first: Lei

last: Huang

first: Shengxian

last: Yuan

first: Zongyan

last: Wang

first: Fangming

last: Gu

first: Zeya

last: Pan

first: Jinzhong

last: Chen

first: Jinrong

last: Qiu

first: Huiying


title: SY-1365, a covalent, first in-class CDK7 inhibitor for cancer treatment

city: Watertown

first: Eric

last: Olson

state: MA

address: 480 Arsenal Street

institute: Syros Pharmaceuticals

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Ablation of ZBTB24 in hematopoietic cells in mice results in antibody deficiency that mimics ICF syndrome

city: Smithville

first: Bin

state: TX

address: 1808 Park Road 1C

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: ICF syndrome, a rare autosomal recessive disorder characterized by immunodeficiency, centromeric instability and facial anomalies, is caused by mutations in DNMT3B, ZBTB24, CDCA7 or HELLS. In this study we show that mice deficient for Zbtb24 in the hematopoietic lineage exhibit a phenotype that recapitulates major clinical features of ICF patients, including hypogammaglobulinemia. RNA-Seq analysis of splenic follicular B cells and marginal zone B cells identifies dozens of genes that show differential expression in the absence of Zbtb24. These include Cdca7, Taf6, Cdc40, Ostc, Crisp3 and Il5ra.

overall_design: Follicular (FO) B cells and marginal zone (MZ) B cells mRNA profiles of 8-12 weeks old VAVcre (Control) and VAVcre-Zbtb24 (CKO) mice

first: Zhengzhou

last: Ying

first: Taiping

first: Kevin

last: McBride


title: SY-1365, a covalent, first in-class CDK7 inhibitor for cancer treatment (ChIP-Seq)

summary:
Recent studies reveal that a subset of cancers in various indications are dependent on high and constant expression of certain transcription factors for growth and survival, a phenomenon termed as transcriptional addiction. Therefore, targeting transcriptional machinery can potentially lead to potent and selective anticancer effects. CDK7 is the catalytic subunit of the CDK-activating kinase (CAK) complex. Its function is required for both cell cycle regulation and transcriptional control of gene expression. CDK7 has recently emerged as an attractive target in cancer since its inhibition leads to decrease of the transcript levels of oncogenic transcription factors, especially those associated with super-enhancers (SEs). Here we describe a first-in-class CDK7 inhibitor SY-1365, which covalently targets a cysteine outside the kinase domain, resulting in sustained, highly selective inhibition of CDK7. In vitro studies reveal that SY-1365 has potency in a wide range of cancer models with low micromolar IC50 values. Cancer cells with low BCL-XL expression are found to be more dependent on MCL1 for survival and therefore particularly sensitive towards SY-1365 treatment since SY-1365 downregulates MCL1 protein level. SY-1365 treatment induces distinct transcriptional changes in acute myeloid leukemia (AML) cell lines. SY-1365 also demonstrates substantial anti-tumor effects in multiple AML xenograft models. Additionally, combination treatment with venetoclax shows synergistic effects in AML models both in vitro and in vivo. Our findings support targeting CDK7 as a new approach for treating transcriptionally addicted cancers. SY-1365 is currently being assessed in a Phase I trial in adult patients (NCT03134638)
We performed microarray based expression profiling to quantify transcriptional changes upon treatment with the CDK7 inhibitor, SY-1365 and to compare it to transcriptional changes induced by treatment with other transcriptional drugs JQ1 (BRD4 inhibitor), NVP2 (CDK9 inhibitor) and flavopiridol (pan-CDK inhibitor). We profiled a human acute myeloid leukemia (AML) cell line  THP-1. Cells were treated with either DMSO, 100nm SY-1365, 25nM NVP2 , 250nM JQ1 or 200nM flavopiridol for two and six hours. All samples were prepared in biological triplicate.

overall_design: ChIP-Seq of H3K27Ac in AML

first: Shanhu

last: Hu

first: Jason

last: Marineau

first: Nisha

last: Rajagopal

first: Kristin

last: Hamman

first: Yoon

last: Choi

first: Darby

last: Schmidt

last: Ke

first: Liv

last: Johannessen

first: Michael

last: Bradley

first: David

last: Orlando

first: Sydney

last: Alnemy

first: Yixuan

last: Ren

first: Stephane

last: Ciblat

first: Dana

last: Winter

first: Anzhelika

last: Kabro

last: Sprott

first: Graeme

last: Hodgson

first: Christian

last: Fritz

first: John

last: Carulli

first: Emmanuelle

last: di Tomaso


title: Glioblastoma Stem Cells Reprogram Chromatin In Vivo To Generate Selective Therapeutic Dependencies

first: Deobrat

last: Dixit


title: Transcriptome profiles of FASTKD knockout cell lines

city: Nedlands

first: Danielle

middle: Louise

last: Rudler

address: 6 Verdun Street

department: Mitochondrial Medicine and Biology

country: Australia

institute: The Kids Research Institute

summary: We explored the effects of different FASTKD protein knockouts on mitochondrial gene expression.

overall_design: Total RNA from human cells was isolated from three control mice (WT) and three of each of the five FASTKD knockout cell lines (KD3, KD4, KD5, KD34, KD45), and was sequenced and analysed for differential expression.

middle: L

first: Aleksandra

last: Filipovska


title: SY-1365, a covalent, first in-class CDK7 inhibitor for cancer treatment (microarray mRNA)

first: Eric

last: Olson

summary: Recent studies reveal that a subset of cancers in various indications are dependent on high and constant expression of certain transcription factors for growth and survival, a phenomenon termed as transcriptional addiction. Therefore, targeting transcriptional machinery can potentially lead to potent and selective anticancer effects. CDK7 is the catalytic subunit of the CDK-activating kinase (CAK) complex. Its function is required for both cell cycle regulation and transcriptional control of gene expression. CDK7 has recently emerged as an attractive target in cancer since its inhibition leads to decrease of the transcript levels of oncogenic transcription factors, especially those associated with super-enhancers (SEs). Here we describe a first-in-class CDK7 inhibitor SY-1365, which covalently targets a cysteine outside the kinase domain, resulting in sustained, highly selective inhibition of CDK7. In vitro studies reveal that SY-1365 has potency in a wide range of cancer models with low micromolar IC50 values. Cancer cells with low BCL-XL expression are found to be more dependent on MCL1 for survival and therefore particularly sensitive towards SY-1365 treatment since SY-1365 downregulates MCL1 protein level. SY-1365 treatment induces distinct transcriptional changes in acute myeloid leukemia (AML) cell lines. SY-1365 also demonstrates substantial anti-tumor effects in multiple AML xenograft models. Additionally, combination treatment with venetoclax shows synergistic effects in AML models both in vitro and in vivo. Our findings support targeting CDK7 as a new approach for treating transcriptionally addicted cancers. SY-1365 is currently being assessed in a Phase I trial in adult patients (NCT03134638)

overall_design: We performed microarray based expression profiling to quantify transcriptional changes upon treatment with the CDK7 inhibitor, SY-1365 and to compare it to transcriptional changes induced by treatment with other transcriptional drugs JQ1 (BRD4 inhibitor), NVP2 (CDK9 inhibitor) and flavopiridol (pan-CDK inhibitor). We profiled a human acute myeloid leukemia (AML) cell line  THP-1. Cells were treated with either DMSO, 100nm SY-1365, 25nM NVP2 , 250nM JQ1 or 200nM flavopiridol for two and six hours. All samples were prepared in biological triplicate.

first: Shanhu

last: Hu

first: Jason

last: Marineau

first: Nisha

last: Rajagopal

first: Kristin

last: Hamman

first: Yoon

last: Choi

last: Schmidt

last: Ke

first: Kevin


title: Expression data of organoid derived from HSCs

city: Busan

first: Sihyung

last: Wang

address: 63-2 Pusandaehak-ro, Kumjeong-gu

department: Integrated Biological Science

country: South Korea

institute: Pusan National University

summary:
To investigate the differences in mRNA expression profiles between TSG-6 or vehicle treated Hu-pHSCs and BM-MSCs organoid spheroids, we performed mRNA microarrays for total RNA extracts isolated from these spheroids (vehicle: CON/3D=3, TSG6: TSG-6/3D=4,  BM: BM-MSCs3D=3)
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: For profiling, we established organoid spheroid as described previously hepatic organoid culture methods.

first: Youngmi

last: Jung


title: Mechanistic Target of Rapamycin Complex 2 (mTORC2) regulation of the primary human trophoblast cell transcriptome

city: Aurora

first: Amy

last: Kelly

state: Colorado

address: 12700 East 19th Avenue, Mail Stop 8613, P.O. Box 6511

institute: University of Colorado

summary: Differential gene expression following the silencing of rictor and raptor to identify genes regulated by mTORC2 in primary human trophoblast (PHT) cells.

overall_design: Whole-genome expression profiling was performed using gene arrays (HumanHT-12 v4 Expression BeadChips, Illumina Inc., San Diego, CA) on RNA isolated from primay human trophoblast cells treated with siRNA sequences to knockdown Rictor, Raptor as well as scramble control (n=4/condition).

first: Fredrick

last: Rosario

middle: C


title: Co-expression network analysis of frontal cortex during the progression of Alzheimer’s disease

status: Public on Oct 15 2021

city: Grand Rapids

first: Betul

last: Kara

state: Michigan

address: 400 Monroe Ave NW

institute: Michigan State University

summary:
Using WGCNA and enrichment analyses to identify pathway level differences between individuals with no cognitive impairment, mild cognitive impairment, and Alzheimer’s disease.
Frozen frontal cortex (BA10) tissue from NCI, MCI, and mild/moderate AD cases (n = 12/group) representing both genders was acquired postmortem from participants in the Rush Religious Orders Study, a longitudinal clinical pathologic study of aging and AD in elderly Catholic clergy

overall_design: Nimblegen expression array human frontal cortex - NCI (No Cognative Impairment) vs. MCI (Mild Cognative Impairment) vs. AD (alzheimers disease);  Labeled cDNA was digested and hybridized to NimbleGen 12 x 135K human arrays for 18 hrs at 42°C and analyzed on a GenePix 4200A scanner (Molecular Devices). Probe intensity levels were quantified with RMA preprocessing (NimbleScan v2.5, Roche)

first: Zachary

middle: B

last: Madaj

first: Karl

last: Dykema

first: Mary

middle: E

last: Winn


title: Gene expression in Fuchs endothelial corneal dystrophy

city: Adelaide

first: Mark

last: Corbett

state: South Australia

address: Adelaide Health and Medical Sciences, University of Adelaide, North Tce

department: Adelaide Medical School

institute: University of Adelaide

summary: Fuchs’ endothelial corneal dystrophy (FECD) is a progressive vision impairing disease caused by thickening of Descemet’s membrane and gradual degeneration and loss of corneal endothelial cells. The aim of this study was to identify differentially expressed genes between FECD-affected and unaffected corneal endothelium to gain insight into the pathophysiological mechanisms underlying this disease. Microarray gene expression analysis was performed on total RNA from FECD-affected and unaffected corneal endothelium-Descemet’s membrane (CE-DM) specimens using the Illumina HumanHT-12 v3.0 expression array. RNA from pools of FECD-affected (n=3 per pool) and individual unaffected (n=3) specimens was used for comparison. Altered expression of a sub-set of differentially expressed genes was validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) in independent specimens. Bioinformatics analysis was performed using InnateDB to reveal functional relationships among the differentially expressed genes and molecular pathways involved in the disease. A total of 16,513 genes were found expressed in the corneal endothelium of which 142 genes were differentially expressed between FECD-affected and unaffected endothelium (log2 fold-change ≥1.5, corrected p-value ≤0.05). Most of the genes were up-regulated (126) and a small proportion down-regulated (16) in affected corneal endothelium. Of the twelve genes prioritised for validation, differential expression of 10 genes, including those ranked 57th and 81st by significance validated by qRT-PCR (8 up-regulated and 2 downregulated, corrected p ≤0.05), one gene showed a trend for up-regulation in affected endothelium, consistent with the microarray analysis and another was up-regulated in an independent study indicating robustness of the differential expression dataset. Bioinformatic analysis revealed significant over-representation of differentially expressed genes in extracellular matrix reorganisation, cellular remodelling, immune response, and inflammation. Network analysis showed functional inter-relatedness of the majority of the dysregulated genes and revealed known direct functional relationships between 20 of the genes; many of these genes have roles in macrophage differentiation, phagocytosis and inflammation. This is the second report of microarray gene expression analysis in FECD. This study revealed a set of highly dysregulated genes in the corneal endothelium in FECD. More than a third of the dysregulated genes in the disease have been discovered for the first time and thus are novel. The dysregulated genes strongly suggest the presence of phagocytic cells, most likely immune cells, and inflammation in corneal endothelium in the disease. This study provides a molecular framework for delineating the mechanisms underlying these cellular processes in FECD.

overall_design: Total RNA was extracted from three pooled diseased (n= 3 per pool) and three individual normal control specimens.

first: Abraham

last: Kuot

first: Richard

last: Mills

first: Grant

last: Snibson

first: Steven

last: Wiffen

first: Raymond

last: Loh

first: Kathryn

last: Burdon

first: Jamie

last: Craig

first: Shiwani

last: Sharma


title: Next Generation Sequencing of H292 cell line cultured with CAFs CM or SL-CAFs CM

city: Wuhan

first: Jing

middle: Shu

last: Meng

address: 1095 Jiefang Avenue, Qiaokou District

department: Union Hospital, Tongji Medical College

institute: Huazhong University of Science and Technology

summary: Cancer cell radioresistance is the primary cause of the decreased curability of non-small cell lung cancer (NSCLC) observed in patients receiving definitive radiotherapy (RT). Following RT, a set of microenvironmental stress responses is triggered, including cell senescence. However, cell senescence is often ignored in designing effective strategies to resolve cancer cell radioresistance. Herein, we identified the senescence-like characteristics of cancer-associated fibroblasts (CAFs) post RT and clarified the formidable ability of senescence-like CAFs in promoting NSCLC cells proliferation and radioresistance through the JAK/STAT pathway. Specific induction of senescence-like CAFs apoptosis using FOXO4-DRI, a FOXO4-p53 interfering peptide, resulted in remarkable effects on radiosensitizing NSCLC cells in vitro and in vivo. In addition, our study also discovered the obvious therapeutic effect of FOXO4-DRI on alleviating radiation-induced pulmonary fibrosis (RIPF) by targeting senescence-like fibroblasts in vivo. In conclusion, by targeting senescence, we offer a new strategy which simultaneously decreases radioresistance of NSCLC and the incidence of RIPF.

overall_design: mRNA profiles of 6 samples (H292 cell line, CAFs CM group and SL-CAFs  CM group, 3 replicates per group).

first: Jingshu

first: Yan

last: Li

first: Chao

last: Wan


title: Transcriptome of bovine induced pluripotent cells (iPSCs)

first: Vimal

last: Selvaraj

summary: This study established the transcriptome of self-renewing, naïve induced pluripotent cells (iPSCs). Reprogramming was performed using Oct4, Sox2, cMyc and Klf4 expression together with SV40LT in bovine embryonic fibroblasts. Colonies were selected and passaged and validated for pluripotency (silencing of exogenous factors, internal markers and differentiation potential). Total RNA was isolated from iPSC colonies (passage 8) derived from three independent reprograming events. Using Poly(A) capture, mRNA was isolated and cDNA libraries prepared using Illumina TruSeq RNA sample Prep Kit and sequenced using Illumina HiSeq 4000. This dataset should serve as a baseline for understanding bovine pluripotency regulation via transcriptional control and signaling.

overall_design: mRNA-sequencing of induced pluripotent cells derived from bovine fibroblasts

first: Viju

last: Pillai

first: Prasanthi

last: Koganti


title: An enhancer-driven stem cell-like program mediated by SOX9 blocks intestinal differentiation in colorectal cancer [v5_chip]

city: Boston

first: Nilay

middle: S

last: Sethi

address: 450 Brookline Ave

department: Department of Medical Oncology

institute: Dana Farber Cancer Institute

summary: Genomic alterations that encourage stem cell activity and hinder proper maturation are central to the development of colorectal cancer (CRC). Key molecular mediators that promote these malignant properties require further elucidation to galvanize translational advances. We therefore aimed to characterize a key factor that blocks intestinal differentiation, define its transcriptional and epigenetic program, and provide preclinical evidence for therapeutic targeting in CRC.

overall_design: Examination of 5 different V5-tagged ChIP experiments with two replicates each. M303 is a truncated version of SOX9.

first: Xiaoyan

last: Liang

first: Gina

last: Duronio

first: Yaying

last: Yang

first: Pratyusha

last: Bala

first: Prajna

last: Hebbar

first: Sandor

last: Spisak

first: Pranshu

last: Sahgal

first: Harshabad

last: Singh

first: Yanxi

last: Zhang

first: Yingtian

last: Xie

first: Paloma

last: Cejas

first: Henry

middle: W

last: Long

first: Adam

last: Bass


title: The MEK5-ERK5 Kinase Axis Controls Lipid Metabolism in Small Cell Lung Cancer

city: Stanford

first: Sandra

last: Cristea

state: California

address: 265 Campus Drive, G2065

department: Cancer Biology

institute: Stanford University

summary: Small cell lung cancer (SCLC), accounts for about 15 percent of all lung cancers, is a neuroendocrine type of carcinoma and is incredibly aggressive, with a dire diagnosis of 5% survival at 5 years. FDA-approved therapies for this disease are almost exclusively limited to chemotherapy and radiotherapy, to which resistance arises within months. Despite global sequencing efforts, few activating mutations have been discovered in SCLC tumors, and targetable alterations account for very small subsets of patients. Due to this lack of a strong oncogenic driver for conventional targeted therapy, SCLC has the potential to benefit from non-oncogene-addiction-based therapeutic approaches. We therefore focused on finding novel non-mutated pathways which could be targetable in SCLC. Restricting our search to kinases, a highly-targetable group of enzymes, we elucidated the active kinome of SCLC and upon identifying MEK5 as a SCLC-specific active kinase, further investigated the role of the MEK5-ERK5 kinase axis in this tumor type. We found that reduction in this axis in both human and murine SCLC cells causes increased susceptibility to apoptosis, and decreased subcutaneous tumor growth in vivo. Transcriptomic analysis of MEK5 and ERK5-knockdown cells showed downregulation of lipid metabolism pathways and SREBP target genes. Based on targeted lipidomics analyses of these same cells, which showed downregulated cholesterol ester species, we focused on the mevalonate arm of the SREBP pathway.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNAseq of murine small-cell lung cancer (SCLC) KP1 cells with MEK5 and ERK5 knockdowns, and control knockdowns (shGFP and shScr), as well as human SCLC cells NJH29 with MEK5 knockdown and control knockdowns (shGFP and shScr)

first: Julia

last: Arand

first: Julien

last: Sage


title: ADAMTSL2 regulates Wnt signaling in myogenesis

city: New York

first: Dirk

last: Hubmacher

state: New York(NY)

address: 1468 Madison Av, Annenberg Building 20-80B

department: Orthopaedics

institute: Icahn School of Medicine at Mount Sinai

summary: ADAMTSL2 mutations cause geleophysic dysplasia, which is characterized by short stature, pseudomuscular build, joint stiffness and tight skin. To elucidate the role of ADAMTSL2 in skeletal muscle myogenesis, we used C2C12 myoblasts, which differentiate and form myotubes when serum is reduced as a model system for myogenesis. Adamtsl2 was depleted by stably expressing shRNA targeting Adamtsl2 mRNA. Upon shRNA-mediated depletion of Adamtsl2, C2C12 myoblasts did not differentiate and did not form myosin heavy chain-positive myotubes in cell culture.

overall_design: Comparison of control and Adamtsl2 depleted C2C12 cells 3 days after onset of differentiation. Adamtsl2 was depleted by stable shRNA overexpression in C2C12 myoblasts. Differentiation was induced by serum-reduction. 3 replicates were analyzed each for control and Adamtsl2 knockdown.

first: Nandaraj

last: Taye


title: Genome-wide maps of gene transcription level of hypoxic Mycobacterium bovis BCG with different c-di-GMP levels

first: Jiaxun

address: Shizishan Road Hongshan District

department: College of Life Science and Technology

institute: Huazhong Agricultural University

summary: Objective of the study is to find out how c-di-GMP regulate bacteria under hypoxic conditions and new c-di-GMP receptors.

sample_organism: Mycobacterium tuberculosis variant bovis BCG

overall_design: Examination of gene expression level in Mycobacterium bovis BCG with different c-di-GMP levels in hypoxia

first: Zhengguo

last: He


status: Public on Oct 14 2021

city: Shanghai

first: hongchuan

last: liu

state: Shanghai

address: NO.826 Zhangheng Road

department: School of Pharmacy

institute: Fudan University

summary:
IL-21-αHSA combined with TIGIT blockade induces an effective anti-tumor immune response, indicated by the significant enrichment of pathways associated with anti-tumor immune response, as well as significantly increased expression of key genes associated with CD8+ T and NK cell cytotoxicity
To further understand the mechanisms by which IL-21-αHSA enhances the benefit of TIGIT blockade, we analyzed MC38 tumor tissues 20 days after five doses of both single agent and combination treatments by RNA sequencing (RNA-seq) of 28,758 genes. Compared to isotype control treatment, combination treatment resulted in 764 genes with differential expression (defined as P < 0.05 and fold change > 2.0), while IL-21-αHSA treatment resulted in 402 DEGs and anti-mTIGIT treatment resulted in 528 DEGs (data not shown). These findings suggest that the combination treatment had a more dramatic effect on gene expression than IL-21-αHSA or anti-mTIGIT treatment alone.  To evaluate the pathways underlying the synergistic anti-tumor efficacy induced by the combination treatment, we performed Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway significance enrichment analysis (defined as P adjust < 0.05). In comparison to the isotype control treatment, 41 KEGG pathways were significantly enriched in the combination treatment group (Table S1) and 31 pathways were significantly enriched in the IL-21-αHSA treatment group (Table S2), of which 28 KEGG enrichment pathways overlapped. Additionally, only 8 KEGG pathways were significantly enriched in the anti-mTIGIT treatment group (Table S3), of which 5 KEGG enrichment pathways overlapped with those of the combination treatment group. These findings suggest that IL-21-αHSA in combination with anti-mTIGIT treatment enriched more KEGG pathways with differential gene expression than for monotherapy, and most of the KEGG pathways significantly enriched by the combination treatment were also differentially enriched by IL-21-αHSA treatment alone. The top 15 pathways, ranked in order of significance, are shown in Fig. 7A. As expected, most are associated with classical anti-tumor immunity signal pathways, including the cytokine-cytokine receptor interaction pathway, the viral protein interaction with cytokine and cytokine receptor pathway, the Th1 and Th2 cell differentiation pathway, the antigen processing and presentation pathway, the T cell receptor signaling pathway, and the PD-L1 expression and PD-1 checkpoint pathway in cancer (P adjust < 0.0001). The natural killer cell mediated cytotoxicity pathway was also significantly enriched (P adjust = 0.0059) in the combination treatment group compared to isotype control treatment group, but was not among the top 15 pathways. Overall, these findings suggest that IL-21-αHSA in combination with TIGIT blockade treatment significantly affects the anti-tumor immunity signal in the tumor micro-environment.  For further verification, we analyzed the gene expression levels of key effector molecules, including Interferon-γ (IFNG), Granzyme A (Gzma), Granzyme B (Gzmb), and Perforin 1 (Prf1), each of which are critical mediators of CD8+ T cell and NK cell cytotoxicity and are known to play critical roles in anti-tumor response. As shown in Fig. 7B-E, the combination treatment significantly increased the expression of all four genes (P < 0.05) relative to isotype control treatment, though only IFNG and Gzma were differentially expressed in the combination treatment group relative to the anti-mTIGIT group (P < 0.05). Collectively, these results suggest that IL-21-αHSA in combination with TIGIT blockade induces an effective anti-tumor immune response, indicated by the significant enrichment of pathways associated with anti-tumor immune response, as well as significantly increased expression of key genes associated with CD8+ T and NK cell cytotoxicity.

overall_design: Group 1: Isotype Control, 3 biological duplicates;  Group 2: IL-21-αHSA, 3 biological duplicates;  Group 3: anti-mTIGIT , 3 biological duplicates;  Group 4: Combination , 3 biological duplicates;

first: Hongchuan

last: Liu

first: Rui

last: Wang

first: Duopeng

last: An

first: Meiqing

last: Feng


title: An enhancer-driven stem cell-like program mediated by SOX9 blocks intestinal differentiation in colorectal cancer [rnaseq_ht115]

first: Nilay

last: Sethi

overall_design: Examination of 6 different SOX9 overexpression RNA-seq experiments with two replicates each. M303 is a truncated version of SOX9.

first: Xiaoyan

last: Liang

first: Gina

last: Duronio

first: Yaying

last: Yang

first: Pratyusha

last: Bala

first: Prajna

last: Hebbar

first: Sandor

last: Spisak

first: Pranshu

last: Sahgal

first: Harshabad

last: Singh

first: Yanxi

middle: J


title: An enhancer-driven stem cell-like program mediated by SOX9 blocks intestinal differentiation in colorectal cancer [h3k27ac]

overall_design: Examination of 5 different H3K27Ac experiments with two replicates each. M303 refers to a truncated version of SOX9.

last: Zhang

first: Yingtian

last: Xie

first: Paloma

last: Cejas

first: Henry

last: Long

first: Adam

last: Bass


title: MicroRNA expression profile in the Laiwu black goat kid liver

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

summary: We sequenced the miRNAs in the liver tissues of goats to further enrich and elucidate the miRNA expression profile in their physiological cycle. The liver tissues were procured at 5-time points from the Laiwu black goats of 1 day, 2 weeks, 4 weeks, 8 weeks, and 12 weeks of age, respectively with 5 goats per time point, for a total of 25 goats. This study identified 1255 miRNAs.

overall_design: The goat kid liver miRNA  profiles  of 1 day, 2 weeks, 4 weeks, 8 weeks, and 12 weeks of age

first: Xiaodong

last: Zhao

first: Tianle

last: Chao

first: Jianmin

last: Wang


title: An enhancer-driven stem cell-like program mediated by SOX9 blocks intestinal differentiation in colorectal cancer [rnaseq_ls180]

first: Nilay

last: Sethi

first: Xiaoyan

last: Liang


title: Loss of TBX3 enhances pancreatic progenitor generation from human pluripotent stem cells

city: Philadelphia

first: Paul

last: Gadue

state: PA

address: 3501 Civic Center Blvd Room 5012

institute: Children's Hospital of Philadelphia

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Loss of TBX3 enhances pancreatic progenitor generation from human pluripotent stem cells [Hepatoblast ATAC-seq]

summary: Tbx3 regulates liver development in the mouse, but it's role in human liver development is unclear. We generated TBX3 knockout pluripotent stem cell lines and found that liver differentiation is also impaired in humans. Interestingly we noted expression of pancreas-specific genes during the liver differentiation in the TBX3 knockout line. To further investigate this phenomenon, we performed ATAC-seq on cells at the hepatoblast stage of the liver differentiation. These studies demonstrated that the loss of TBX3 enhances pancreatic-gene signature, implicating TBX3 as a regulator of fate decisions.

overall_design: Wildtype and TBX3 knockout plurpotent stem cells lines were differentiated to hepatocytes. Chromatin accesibility was examined at the heptoblast stage of the liver differentiation (Day 12 Hepatoblast stage). Two biological replicates were analyzed for each stage (two genotypes, one stage per genotype)

first: Somdutta

last: Mukherjee

first: Deborah

last: French